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@ARTICLE{Liu:275263,
      author       = {Y. Liu and J. Klein and R. Bajpai and L. Dong and Q. Tran
                      and P. Kolekar and J. L. Smith and R. E. Ries and B. J.
                      Huang and Y.-C. Wang and T. A. Alonzo and L. Tian and H. L.
                      Mulder and T. I. Shaw and J. Ma and M. P. Walsh and G. Song
                      and T. Westover and R. J. Autry$^*$ and A. M. Gout and D. A.
                      Wheeler and S. Wan and G. Wu and J. J. Yang and W. E. Evans
                      and M. Loh and J. Easton and J. Zhang and J. M. Klco and S.
                      Meshinchi and P. A. Brown and S. M. Pruett-Miller and X. Ma},
      title        = {{E}tiology of oncogenic fusions in 5,190 childhood cancers
                      and its clinical and therapeutic implication.},
      journal      = {Nature Communications},
      volume       = {14},
      number       = {1},
      issn         = {2041-1723},
      address      = {[London]},
      publisher    = {Nature Publishing Group UK},
      reportid     = {DKFZ-2023-00710},
      pages        = {1739},
      year         = {2023},
      abstract     = {Oncogenic fusions formed through chromosomal rearrangements
                      are hallmarks of childhood cancer that define cancer
                      subtype, predict outcome, persist through treatment, and can
                      be ideal therapeutic targets. However, mechanistic
                      understanding of the etiology of oncogenic fusions remains
                      elusive. Here we report a comprehensive detection of 272
                      oncogenic fusion gene pairs by using tumor transcriptome
                      sequencing data from 5190 childhood cancer patients. We
                      identify diverse factors, including translation frame,
                      protein domain, splicing, and gene length, that shape the
                      formation of oncogenic fusions. Our mathematical modeling
                      reveals a strong link between differential selection
                      pressure and clinical outcome in CBFB-MYH11. We discover 4
                      oncogenic fusions, including RUNX1-RUNX1T1, TCF3-PBX1,
                      CBFA2T3-GLIS2, and KMT2A-AFDN, with promoter-hijacking-like
                      features that may offer alternative strategies for
                      therapeutic targeting. We uncover extensive alternative
                      splicing in oncogenic fusions including KMT2A-MLLT3,
                      KMT2A-MLLT10, C11orf95-RELA, NUP98-NSD1, KMT2A-AFDN and
                      ETV6-RUNX1. We discover neo splice sites in 18 oncogenic
                      fusion gene pairs and demonstrate that such splice sites
                      confer therapeutic vulnerability for etiology-based genome
                      editing. Our study reveals general principles on the
                      etiology of oncogenic fusions in childhood cancer and
                      suggests profound clinical implications including
                      etiology-based risk stratification and genome-editing-based
                      therapeutics.},
      cin          = {B062},
      ddc          = {500},
      cid          = {I:(DE-He78)B062-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:37019972},
      doi          = {10.1038/s41467-023-37438-4},
      url          = {https://inrepo02.dkfz.de/record/275263},
}